fix step to be acted on when cleaning up snp_calling_gatk_haplotype_caller pipeline
apply_recalibration_mode option should not flow through to the frontend
Merge branch 'develop' of /software/vertres/git/origin/vr-pipe into develop
add general vqsr pipeline and fix description of vqsr_for_snps pipeline
platform field in bam headers should be one of ILLUMINA,LS454,ABI_SOLID